Full wwPDB X-ray Structure Validation Report i ○ Mar 14, 2018 – 12:02 am GMT PDB ID : 3W4Q Title : Crystal structure of PenA beta-lactamase from Burkholderia multivorans at pH4.2 Authors : Nukaga, M.; Ohuchi, N.; Papp-Wallace, K.M.; Taracila, M.A.; Bonomo, R.A. Deposited on : 2013-01-10 Resolution : 1.20 Å(reported) This is a Full wwPDB X-ray Structure Validation Report for a publicly released PDB entry. We welcome your comments at [email protected]A user guide is available at https://www.wwpdb.org/validation/2017/XrayValidationReportHelp with specific help available everywhere you see the i ○ symbol. The following versions of software and data (see references i ○) were used in the production of this report: MolProbity : 4.02b-467 Xtriage (Phenix) : 1.13 EDS : trunk31020 Percentile statistics : 20171227.v01 (using entries in the PDB archive December 27th 2017) Refmac : 5.8.0158 CCP4 : 7.0 (Gargrove) Ideal geometry (proteins) : Engh & Huber (2001) Ideal geometry (DNA, RNA) : Parkinson et al. (1996) Validation Pipeline (wwPDB-VP) : trunk31020
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Full wwPDB X-ray Structure Validation Report i○
Mar 14, 2018 – 12:02 am GMT
PDB ID : 3W4QTitle : Crystal structure of PenA beta-lactamase from Burkholderia multivorans at
Page 2 Full wwPDB X-ray Structure Validation Report 3W4Q
1 Overall quality at a glance i○
The following experimental techniques were used to determine the structure:X-RAY DIFFRACTION
The reported resolution of this entry is 1.20 Å.
Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown inthe following graphic. The table shows the number of entries on which the scores are based.
The table below summarises the geometric issues observed across the polymeric chains and their fitto the electron density. The red, orange, yellow and green segments on the lower bar indicate thefraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. Agrey segment represents the fraction of residues that are not modelled. The numeric value for eachfraction is indicated below the corresponding segment, with a dot representing fractions <=5%The upper red bar (where present) indicates the fraction of residues that have poor fit to theelectron density. The numeric value is given above the bar.
Page 3 Full wwPDB X-ray Structure Validation Report 3W4Q
2 Entry composition i○
There are 2 unique types of molecules in this entry. The entry contains 6968 atoms, of which 0are hydrogens and 0 are deuteriums.
In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occu-pancy, the AltConf column contains the number of residues with at least one atom in alternateconformation and the Trace column contains the number of residues modelled with at most 2atoms.
Page 4 Full wwPDB X-ray Structure Validation Report 3W4Q
3 Residue-property plots i○
These plots are drawn for all protein, RNA and DNA chains in the entry. The first graphic fora chain summarises the proportions of the various outlier classes displayed in the second graphic.The second graphic shows the sequence view annotated by issues in geometryand electron density.Residues are color-coded according to the number of geometric quality criteria for which theycontain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. A red dotabove a residue indicates a poor fit to the electron density (RSRZ > 2). Stretches of 2 or moreconsecutive residues without any outlier are shown as a green connector. Residues present in thesample, but not in the model, are shown in grey.
0.027 for -1/2*h-3/2*k,-1/2*h+1/2*k,-l0.028 for -1/2*h+3/2*k,1/2*h+1/2*k,-l0.488 for 1/2*h-3/2*k,-1/2*h-1/2*k,-l0.489 for 1/2*h+3/2*k,1/2*h-1/2*k,-l
0.027 for -h,-k,l
Xtriage
Fo,Fc correlation 0.98 EDSTotal number of atoms 6968 wwPDB-VP
Average B, all atoms (Å2) 18.0 wwPDB-VP
Xtriage’s analysis on translational NCS is as follows: The largest off-origin peak in the Pattersonfunction is 5.92% of the height of the origin peak. No significant pseudotranslation is detected.
1Intensities estimated from amplitudes.2Theoretical values of < |L| >, < L2 > for acentric reflections are 0.5, 0.333 respectively for untwinned datasets,
Page 6 Full wwPDB X-ray Structure Validation Report 3W4Q
5 Model quality i○
5.1 Standard geometry i○
The Z score for a bond length (or angle) is the number of standard deviations the observed valueis removed from the expected value. A bond length (or angle) with |Z| > 5 is considered anoutlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (orangles).
Mol Chain Bond lengths Bond anglesRMSZ #|Z| >5 RMSZ #|Z| >5
1 A 0.67 0/2096 1.44 39/2855 (1.4%)1 B 0.69 0/2069 1.45 34/2819 (1.2%)1 C 0.67 0/2093 1.47 28/2849 (1.0%)All All 0.67 0/6258 1.46 101/8523 (1.2%)
There are no bond length outliers.
All (101) bond angle outliers are listed below:
Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 C 161 ARG NE-CZ-NH1 -16.14 112.23 120.301 A 161 ARG NE-CZ-NH1 -15.92 112.34 120.301 B 161 ARG NE-CZ-NH1 -15.57 112.52 120.301 C 204[A] ARG NE-CZ-NH1 15.23 127.92 120.301 C 204[B] ARG NE-CZ-NH1 15.23 127.92 120.301 C 204[A] ARG CD-NE-CZ 13.40 142.36 123.601 C 204[B] ARG CD-NE-CZ 13.40 142.36 123.601 B 191[A] ARG NE-CZ-NH2 -12.89 113.86 120.301 B 191[B] ARG NE-CZ-NH2 -12.89 113.86 120.301 A 141[A] ARG NE-CZ-NH1 12.78 126.69 120.301 A 141[B] ARG NE-CZ-NH1 12.78 126.69 120.301 C 191[B] ARG NE-CZ-NH2 -11.94 114.33 120.301 C 191[C] ARG NE-CZ-NH2 -11.94 114.33 120.301 B 57 ARG NE-CZ-NH2 -11.40 114.60 120.301 A 57 ARG CD-NE-CZ 10.15 137.81 123.601 C 57 ARG NE-CZ-NH2 -9.76 115.42 120.301 A 161 ARG NH1-CZ-NH2 9.51 129.86 119.401 C 94 ARG NE-CZ-NH1 9.49 125.04 120.301 B 212 ARG NE-CZ-NH2 -9.46 115.57 120.301 A 153 ARG NE-CZ-NH2 -9.10 115.75 120.301 A 153 ARG NE-CZ-NH1 8.99 124.80 120.301 B 94 ARG NE-CZ-NH1 8.90 124.75 120.301 B 168 GLU OE1-CD-OE2 8.70 133.74 123.301 B 161 ARG NH1-CZ-NH2 8.48 128.73 119.40
Page 7 Full wwPDB X-ray Structure Validation Report 3W4Q
Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 A 191[A] ARG NE-CZ-NH2 -8.37 116.11 120.301 A 191[B] ARG NE-CZ-NH2 -8.37 116.11 120.301 B 153 ARG NE-CZ-NH2 -8.24 116.18 120.301 B 44 ARG NE-CZ-NH2 -8.24 116.18 120.301 A 222 ARG NE-CZ-NH1 8.15 124.37 120.301 B 277 ASP CB-CG-OD1 7.98 125.48 118.301 C 161 ARG NH1-CZ-NH2 7.74 127.92 119.401 B 256[A] ARG NE-CZ-NH2 -7.66 116.47 120.301 B 256[B] ARG NE-CZ-NH2 -7.66 116.47 120.301 C 158 ASP CB-CG-OD2 7.63 125.17 118.301 B 61 ARG NE-CZ-NH2 -7.48 116.56 120.301 B 111 ARG CD-NE-CZ 7.46 134.05 123.601 C 114 ASP CB-CG-OD1 7.45 125.01 118.301 B 44 ARG NE-CZ-NH1 7.42 124.01 120.301 C 204[A] ARG NH1-CZ-NH2 -7.42 111.23 119.401 C 204[B] ARG NH1-CZ-NH2 -7.42 111.23 119.401 A 168 GLU OE1-CD-OE2 7.39 132.17 123.301 A 44 ARG NE-CZ-NH1 7.32 123.96 120.301 B 141[A] ARG NE-CZ-NH1 7.16 123.88 120.301 B 141[B] ARG NE-CZ-NH1 7.16 123.88 120.301 B 164 ARG NE-CZ-NH2 -7.15 116.72 120.301 B 277 ASP CB-CG-OD2 -7.10 111.91 118.301 B 57 ARG NE-CZ-NH1 7.07 123.83 120.301 A 44 ARG NE-CZ-NH2 -6.96 116.82 120.301 A 114 ASP CB-CG-OD1 6.93 124.53 118.301 A 178 ARG NE-CZ-NH1 -6.70 116.95 120.301 B 160 PHE CB-CG-CD1 6.68 125.47 120.801 C 191[B] ARG NH1-CZ-NH2 6.62 126.69 119.401 C 191[C] ARG NH1-CZ-NH2 6.62 126.69 119.401 C 284 ARG NE-CZ-NH2 -6.55 117.03 120.301 A 57 ARG NE-CZ-NH2 -6.49 117.05 120.301 B 99 ARG CD-NE-CZ 6.48 132.68 123.601 C 63 ASP CB-CG-OD1 6.25 123.93 118.301 C 111 ARG CD-NE-CZ 6.20 132.28 123.601 B 178 ARG NE-CZ-NH2 -6.18 117.21 120.301 B 269 ARG NE-CZ-NH2 6.17 123.39 120.301 A 204[A] ARG NE-CZ-NH2 6.17 123.38 120.301 A 204[B] ARG NE-CZ-NH2 6.17 123.38 120.301 A 111 ARG CD-NE-CZ 6.12 132.17 123.601 A 277 ASP CB-CG-OD1 6.01 123.71 118.301 C 39 ARG NE-CZ-NH2 -5.93 117.33 120.301 A 222 ARG NE-CZ-NH2 -5.88 117.36 120.30
Continued on next page...
Page 8 Full wwPDB X-ray Structure Validation Report 3W4Q
Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 C 222 ARG NE-CZ-NH1 5.72 123.16 120.301 A 105 TYR CG-CD2-CE2 5.70 125.86 121.301 C 269 ARG NE-CZ-NH1 5.70 123.15 120.301 C 164 ARG NE-CZ-NH1 5.66 123.13 120.301 A 114 ASP OD1-CG-OD2 -5.65 112.57 123.301 A 86 ALA CB-CA-C -5.57 101.74 110.101 B 212 ARG NH1-CZ-NH2 5.55 125.50 119.401 A 284 ARG CD-NE-CZ 5.53 131.34 123.601 C 57 ARG CD-NE-CZ 5.50 131.31 123.601 C 39 ARG NE-CZ-NH1 5.48 123.04 120.301 A 97 TYR CG-CD1-CE1 5.44 125.65 121.301 B 227[A] THR C-N-CA 5.36 133.54 122.301 B 227[B] THR C-N-CA 5.36 133.54 122.301 A 141[A] ARG NE-CZ-NH2 -5.33 117.64 120.301 A 141[B] ARG NE-CZ-NH2 -5.33 117.64 120.301 A 57 ARG NE-CZ-NH1 5.32 122.96 120.301 B 105 TYR CG-CD2-CE2 5.30 125.54 121.301 B 204 ARG NE-CZ-NH2 5.26 122.93 120.301 A 111 ARG NE-CZ-NH1 5.24 122.92 120.301 C 86 ALA CB-CA-C -5.21 102.29 110.101 A 86 ALA N-CA-CB 5.18 117.36 110.101 A 264 TYR CB-CG-CD2 5.17 124.10 121.001 C 51 ASP CB-CG-OD1 5.14 122.93 118.301 A 111 ARG NE-CZ-NH2 -5.14 117.73 120.301 A 114 ASP CB-CG-OD2 5.11 122.90 118.301 A 161 ARG NE-CZ-NH2 -5.10 117.75 120.301 C 115 THR O-C-N -5.08 114.56 123.201 A 197 ASP CB-CG-OD2 -5.08 113.73 118.301 A 94 ARG NE-CZ-NH1 5.07 122.84 120.301 B 51 ASP CB-CG-OD1 5.07 122.86 118.301 A 97 TYR CB-CG-CD2 5.04 124.02 121.001 A 284 ARG NE-CZ-NH2 -5.04 117.78 120.301 B 86 ALA CB-CA-C -5.02 102.57 110.101 B 39 ARG CD-NE-CZ 5.02 130.63 123.601 B 93 GLN OE1-CD-NE2 5.02 133.45 121.90
There are no chirality outliers.
There are no planarity outliers.
Page 9 Full wwPDB X-ray Structure Validation Report 3W4Q
5.2 Too-close contacts i○
In the following table, the Non-H and H(model) columns list the number of non-hydrogen atomsand hydrogen atoms in the chain respectively. The H(added) column lists the number of hydrogenatoms added and optimized by MolProbity. The Clashes column lists the number of clashes withinthe asymmetric unit, whereas Symm-Clashes lists symmetry related clashes.
Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes1 A 2019 0 2035 13 01 B 2004 0 2019 10 01 C 2016 0 2035 8 02 A 299 0 0 4 02 B 312 0 0 6 02 C 318 0 0 2 0All All 6968 0 6089 27 0
The all-atom clashscore is defined as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 2.
All (27) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.
In the following table, the Percentiles column shows the percent Ramachandran outliers of thechain as a percentile score with respect to all X-ray entries followed by that with respect to entriesof similar resolution.
The Analysed column shows the number of residues for which the backbone conformation wasanalysed, and the total number of residues.
All All 820/774 (106%) 810 (99%) 10 (1%) 0 100 100
There are no Ramachandran outliers to report.
5.3.2 Protein sidechains i○
In the following table, the Percentiles column shows the percent sidechain outliers of the chain as apercentile score with respect to all X-ray entries followed by that with respect to entries of similarresolution.
The Analysed column shows the number of residues for which the sidechain conformation wasanalysed, and the total number of residues.
Mol Chain Analysed Rotameric Outliers Percentiles
1 A 205/193 (106%) 202 (98%) 3 (2%) 67 31
1 B 202/193 (105%) 200 (99%) 2 (1%) 78 49Continued on next page...
Page 13 Full wwPDB X-ray Structure Validation Report 3W4Q
6 Fit of model and data i○
6.1 Protein, DNA and RNA chains i○
In the following table, the column labelled ‘#RSRZ> 2’ contains the number (and percentage)of RSRZ outliers, followed by percent RSRZ outliers for the chain as percentile scores relative toall X-ray entries and entries of similar resolution. The OWAB column contains the minimum,median, 95th percentile and maximum values of the occupancy-weighted average B-factor perresidue. The column labelled ‘Q< 0.9’ lists the number of (and percentage) of residues with anaverage occupancy less than 0.9.